def test_overlap_experiment_annotation(self):
epidb = DeepBlueClient(address="localhost", port=31415)
self.init_base(epidb)
sample_id = self.sample_ids[0]
self.insert_experiment(epidb, "hg19_chr1_1", sample_id)
self.insert_annotation(epidb, "Cpg Islands")
# TODO: Is this test actually check anything?
res, qid_1 = epidb.select_regions("hg19_chr1_1", "hg19", "Methylation",
sample_id, "tech1", "ENCODE", "chr1",
760000, 860000, self.admin_key)
self.assertSuccess(res, qid_1)
res, req = epidb.count_regions(qid_1, self.admin_key)
self.assertSuccess(res, req)
count = self.count_request(req)
res, qid_2 = epidb.select_annotations("Cpg Islands", "hg19", "chr1",
None, None, self.admin_key)
self.assertSuccess(res, qid_2)
res, req = epidb.count_regions(qid_2, self.admin_key)
self.assertSuccess(res, req)
count = self.count_request(req)
res, qid_3 = epidb.merge_queries(qid_1, qid_2, self.admin_key)
self.assertSuccess(res, qid_3)
res, req = epidb.count_regions(qid_3, self.admin_key)
self.assertSuccess(res, req)
count = self.count_request(req)
def test_merge_tiling(self):
epidb = DeepBlueClient(address="localhost", port=31415)
self.init_full(epidb)
res, qid1 = epidb.tiling_regions(10000, "hg19", "chr1", self.admin_key)
self.assertSuccess(res, qid1)
res, qid2 = epidb.select_regions("hg19_chr1_1", "hg19", None, None, None, None, None, None, None, self.admin_key)
self.assertSuccess(res, qid2)
# limit the tilings on the range of the experiment
res, qid3 = epidb.filter_regions(qid1, "START", ">=", "713240", "number", self.admin_key)
self.assertSuccess(res, qid3)
res, qid4 = epidb.filter_regions(qid3, "END", "<=", "876330", "number", self.admin_key)
self.assertSuccess(res, qid4)
res, qid5 = epidb.merge_queries(qid4, qid2, self.admin_key)
self.assertSuccess(res, qid5)
res, req = epidb.get_regions(qid5, "CHROMOSOME,START,END", self.admin_key)
self.assertSuccess(res, req)
regions = self.get_regions_request(req)
expected_regions = helpers.get_result("merge_tiling")
self.assertEqual(regions, expected_regions)
def test_experiment_name_metacolumn2(self):
epidb = DeepBlueClient(address="localhost", port=31415)
self.init_base()
self.insert_experiment(epidb, "hg19_chr1_1")
self.insert_experiment(epidb, "hg19_chr1_2")
res, qid1 = epidb.select_regions("hg19_chr1_2", "hg19", None, None,
None, None, None, 750000, 770000,
self.admin_key)
self.assertSuccess(res, qid1)
res, qid2 = epidb.select_regions("hg19_chr1_1", "hg19", None, None,
None, None, None, 750000, 770000,
self.admin_key)
self.assertSuccess(res, qid2)
res, qid3 = epidb.merge_queries(qid1, qid2, self.admin_key)
self.assertSuccess(res, qid3)
expected = helpers.get_result("experiment_name_multiple_experiments")
res, req = epidb.get_regions(qid3, "CHROMOSOME,START,END,@NAME",
self.admin_key)
self.assertSuccess(res, req)
regions = self.get_regions_request(req)
l_regions = regions.split("\n")
l_expected = expected.split("\n")
self.assertEqual(set(l_regions), set(l_expected))
def test_multiple_merge(self):
epidb = DeepBlueClient(address="localhost", port=31415)
self.init_base(epidb)
sizes = [10000, 20000, 25000, 30000, 35000, 40000, 50000]
qs = []
for s in sizes:
res, q_t = epidb.tiling_regions(s, "hg19", "chr21", self.admin_key)
qs.append(q_t)
res, qid_3 = epidb.merge_queries(qs[0], qs[1:], self.admin_key)
self.assertSuccess(res, qid_3)
res, req = epidb.count_regions(qid_3, self.admin_key)
self.assertSuccess(res, req)
count = self.count_request(req)
self.assertEqual(count, 14287)
def test_complex1(self):
epidb = DeepBlueClient(address="localhost", port=31415)
self.init_full(epidb)
res, qid_1_1 = epidb.select_regions("hg19_chr1_1", "hg19", None, None,
None, None, None, None, None,
self.admin_key)
#server.get_regions(qid_1_1, )
self.assertSuccess(res, qid_1_1)
res, qid_1_2 = epidb.select_regions("hg19_chr1_2", "hg19", None, None,
None, None, None, None, None,
self.admin_key)
self.assertSuccess(res, qid_1_2)
res, qid_2 = epidb.merge_queries(qid_1_1, qid_1_2, self.admin_key)
self.assertSuccess(res, qid_2)
res, regions = epidb.get_regions(qid_2, "CHROMOSOME,START,END",
self.admin_key)
self.assertSuccess(res, regions)
res, qid_1_3 = epidb.select_regions("hg19_chr1_3", "hg19", None, None,
None, None, None, None, None,
self.admin_key)
self.assertSuccess(res, qid_1_3)
res, qid_5 = epidb.intersection(qid_2, qid_1_3, self.admin_key)
self.assertSuccess(res, qid_5)
res, req = epidb.get_regions(
qid_5,
"CHROMOSOME,START,END,NAME,SCORE,STRAND,SIGNAL_VALUE,P_VALUE,Q_VALUE,PEAK",
self.admin_key)
self.assertSuccess(res, req)
regions = self.get_regions_request(req)
expected_regions = helpers.get_result("complex1")
self.assertEqual(
regions.split("\n").sort(),
expected_regions.split("\n").sort())
def test_merge_queries(self):
epidb = DeepBlueClient(address="localhost", port=31415)
self.init_full(epidb)
res, qid_1 = epidb.select_experiments("hg19_chr1_1", None, 760000,
860000, self.admin_key)
self.assertSuccess(res, qid_1)
res, qid_2 = epidb.select_regions("hg19_chr1_2", "hg19", None, None,
None, None, None, 760000, 860000,
self.admin_key)
self.assertSuccess(res, qid_2)
res, qid_3 = epidb.merge_queries(qid_1, qid_2, self.admin_key)
self.assertSuccess(res, qid_3)
expected_regions = helpers.get_result("merge_760k_860k")
res, req = epidb.get_regions(qid_3, "CHROMOSOME,START,END",
self.admin_key)
self.assertSuccess(res, req)
regions = self.get_regions_request(req)
self.assertEqual(regions, expected_regions)
def test_complex2(self):
epidb = DeepBlueClient(address="localhost", port=31415)
self.init_full(epidb)
self.insert_experiment(epidb, "hg19_big_1")
self.insert_experiment(epidb, "hg19_big_2")
res, qid_1_1 = epidb.select_regions("hg19_big_1", "hg19", None, None,
None, None, None, 1000000, 3000000,
self.admin_key)
self.assertSuccess(res, qid_1_1)
res, req = epidb.count_regions(qid_1_1, self.admin_key)
self.assertSuccess(res, req)
c = self.count_request(req)
res, qid_1_2 = epidb.select_regions(
"hg19_big_1", "hg19", None, None, None, None,
["chr1", "chr3", "chr11", "chrX", "chr9"], None, None,
self.admin_key)
self.assertSuccess(res, qid_1_2)
res, req = epidb.count_regions(qid_1_2, self.admin_key)
self.assertSuccess(res, req)
c = self.count_request(req)
# this gives us regions from 1,000,000 to 3,000,000 on chromosomes chr1, chr3, chr9, chr11, chrY
res, qid_2_1 = epidb.intersection(qid_1_1, qid_1_2, self.admin_key)
self.assertSuccess(res, qid_2_1)
res, req = epidb.count_regions(qid_2_1, self.admin_key)
self.assertSuccess(res, req)
c = self.count_request(req)
self.assertEqual(c, 247)
res, qid_2_2 = epidb.tiling_regions(1000, "hg19",
["chr1", "chr2", "chr15", "chrX"],
self.admin_key)
self.assertSuccess(res, qid_2_2)
res, req = epidb.count_regions(qid_2_2, self.admin_key)
self.assertSuccess(res, req)
c = self.count_request(req)
res, qid_3_1 = epidb.merge_queries(qid_2_1, qid_2_2, self.admin_key)
self.assertSuccess(res, qid_3_1)
res, req = epidb.count_regions(qid_3_1, self.admin_key)
self.assertSuccess(res, req)
c = self.count_request(req)
res, qid_4_1 = epidb.filter_regions(qid_3_1, "START", ">=", "2000000",
"number", self.admin_key)
self.assertSuccess(res, qid_4_1)
res, req = epidb.count_regions(qid_4_1, self.admin_key)
self.assertSuccess(res, req)
c = self.count_request(req)
res, qid_4_2 = epidb.select_regions("hg19_big_2", "hg19", None, None,
None, None, ["chr1", "chrX"], None,
None, self.admin_key)
self.assertSuccess(res, qid_4_2)
(res, qid_4_2_cached) = epidb.query_cache(qid_4_2, True,
self.admin_key)
res, req = epidb.count_regions(qid_4_2_cached, self.admin_key)
self.assertSuccess(res, req)
c = self.count_request(req)
self.assertEqual(c, 8961)
res, qid_5_1 = epidb.intersection(qid_4_1, qid_4_2_cached,
self.admin_key)
self.assertSuccess(res, qid_5_1)
res, req = epidb.count_regions(qid_5_1, self.admin_key)
self.assertSuccess(res, req)
count = self.count_request(req)
self.assertEqual(count, 14356)
res, qid_6_1 = epidb.filter_regions(qid_5_1, "END", "<", "2200000",
"number", self.admin_key)
self.assertSuccess(res, qid_6_1)
(res, qid_6_1_cached) = epidb.query_cache(qid_6_1, True,
self.admin_key)
res, req = epidb.count_regions(qid_6_1, self.admin_key)
self.assertSuccess(res, req)
count = self.count_request(req)
self.assertEqual(count, 52)
res, req = epidb.get_regions(
qid_6_1,
"CHROMOSOME,START,END,NAME,SCORE,STRAND,SIGNAL_VALUE,P_VALUE,Q_VALUE,PEAK,@NAME",
self.admin_key)
self.assertSuccess(res, req)
regions = self.get_regions_request(req)
expected_regions = helpers.get_result("complex2")
self.assertEqual(regions, expected_regions)
